Introduction

Data from Sophie’s samples (human cells)

Volcano plot

GSEA analysis

Gene set enrichment analysis using - pval < 0,05 - pval < 0,001

Filtering on pval < 0,05

Gene ontology (Biological process and Molecular function)

ID setSize NES p.adjust qvalue
GOBP_REGULATION_OF_CELLULAR_COMPONENT_MOVEMENT 182 2.158904 0.0010628 0.0009356
GOBP_REGULATION_OF_VASCULATURE_DEVELOPMENT 55 2.377661 0.0013660 0.0012024
GOBP_RESPONSE_TO_PURINE_CONTAINING_COMPOUND 23 2.328951 0.0091467 0.0080518
GOBP_REGULATION_OF_EPITHELIAL_CELL_MIGRATION 37 2.278847 0.0091467 0.0080518
GOBP_POSITIVE_REGULATION_OF_LOCOMOTION 107 2.116812 0.0091467 0.0080518
GOBP_AMEBOIDAL_TYPE_CELL_MIGRATION 71 2.101033 0.0091467 0.0080518
GOBP_POSITIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II 286 1.805991 0.0091467 0.0080518
GOBP_CELL_MIGRATION 263 1.793768 0.0091467 0.0080518
GOBP_TISSUE_MIGRATION 53 2.192531 0.0093384 0.0082206
GOBP_NEGATIVE_REGULATION_OF_RESPONSE_TO_STIMULUS 347 1.728661 0.0093384 0.0082206
GOBP_MATERNAL_PLACENTA_DEVELOPMENT 12 2.234071 0.0097947 0.0086223
GOBP_NERVOUS_SYSTEM_PROCESS 149 -1.975748 0.0097947 0.0086223
GOBP_CELLULAR_RESPONSE_TO_ENDOGENOUS_STIMULUS 285 1.752879 0.0097947 0.0086223
GOBP_POSITIVE_REGULATION_OF_VASCULATURE_DEVELOPMENT 30 2.252706 0.0103605 0.0091204
GOBP_MATERNAL_PROCESS_INVOLVED_IN_FEMALE_PREGNANCY 16 2.186883 0.0103605 0.0091204
GOBP_OXIDATIVE_PHOSPHORYLATION 74 -2.121510 0.0103605 0.0091204
GOBP_NEGATIVE_REGULATION_OF_CELL_DIFFERENTIATION 118 1.934489 0.0103605 0.0091204
GOBP_TRANSMEMBRANE_TRANSPORT 289 -1.727893 0.0103605 0.0091204
GOBP_LOCOMOTION 330 1.701054 0.0103605 0.0091204
GOBP_POSITIVE_REGULATION_OF_EPITHELIAL_CELL_MIGRATION 27 2.220117 0.0113617 0.0100017
GOBP_POSITIVE_REGULATION_OF_RNA_METABOLIC_PROCESS 462 1.611512 0.0118857 0.0104630
GOBP_NADH_DEHYDROGENASE_COMPLEX_ASSEMBLY 31 -2.233059 0.0125085 0.0110112
GOBP_NEGATIVE_REGULATION_OF_DEVELOPMENTAL_PROCESS 167 1.856175 0.0160352 0.0141158
GOBP_INORGANIC_ION_TRANSMEMBRANE_TRANSPORT 150 -1.907533 0.0166576 0.0146637
GOBP_INFLAMMATORY_RESPONSE 149 1.872661 0.0166576 0.0146637
GOBP_ION_TRANSMEMBRANE_TRANSPORT 202 -1.833908 0.0166576 0.0146637
GOBP_NEURON_PROJECTION_GUIDANCE 20 -2.222593 0.0169168 0.0148919
GOBP_MITOCHONDRIAL_ELECTRON_TRANSPORT_NADH_TO_UBIQUINONE 32 -2.238387 0.0169425 0.0149145
GOBP_REGULATION_OF_ANATOMICAL_STRUCTURE_MORPHOGENESIS 167 1.840059 0.0169425 0.0149145
GOBP_PROTON_TRANSMEMBRANE_TRANSPORT 56 -2.059081 0.0180886 0.0159234
GOBP_NEGATIVE_REGULATION_OF_MAP_KINASE_ACTIVITY 24 2.102521 0.0186570 0.0164237
GOBP_MITOCHONDRIAL_RESPIRATORY_CHAIN_COMPLEX_ASSEMBLY 50 -2.088816 0.0186570 0.0164237
GOBP_NEGATIVE_REGULATION_OF_MULTICELLULAR_ORGANISMAL_PROCESS 181 1.811724 0.0186570 0.0164237
GOBP_SENSORY_PERCEPTION 75 -1.997401 0.0192393 0.0169363
GOBP_EPITHELIAL_CELL_PROLIFERATION 63 2.008819 0.0209139 0.0184105
GOBP_STRIATED_MUSCLE_CELL_PROLIFERATION 12 2.116013 0.0212855 0.0187377
GOBP_RESPONSE_TO_STEROID_HORMONE 85 1.912972 0.0221553 0.0195033
GOBP_RESPONSE_TO_CAMP 14 2.129923 0.0250854 0.0220826
GOBP_TISSUE_REGENERATION 16 2.085994 0.0250854 0.0220826
GOBP_ATP_SYNTHESIS_COUPLED_PROTON_TRANSPORT 14 -2.158991 0.0253989 0.0223586
GOBP_ATP_BIOSYNTHETIC_PROCESS 23 -2.127332 0.0253989 0.0223586
GOBP_RAS_PROTEIN_SIGNAL_TRANSDUCTION 87 1.946354 0.0253989 0.0223586
GOBP_DEVELOPMENTAL_GROWTH 120 1.857243 0.0253989 0.0223586
GOBP_RESPONSE_TO_ENDOGENOUS_STIMULUS 345 1.569007 0.0253989 0.0223586
GOBP_MITOCHONDRIAL_ATP_SYNTHESIS_COUPLED_PROTON_TRANSPORT 11 -2.076761 0.0264326 0.0232686
GOBP_ENDOTHELIAL_CELL_MIGRATION 39 2.043009 0.0269058 0.0236852
GOBP_RETINA_DEVELOPMENT_IN_CAMERA_TYPE_EYE 18 2.110079 0.0273758 0.0240989
GOBP_RESPONSE_TO_LEUKEMIA_INHIBITORY_FACTOR 27 2.076573 0.0273758 0.0240989
GOBP_POSITIVE_REGULATION_OF_MIRNA_TRANSCRIPTION 11 2.039111 0.0273758 0.0240989
GOBP_NEGATIVE_REGULATION_OF_SIGNALING 296 1.641383 0.0273758 0.0240989
GOBP_GROWTH 203 1.718381 0.0280495 0.0246920
GOBP_ION_TRANSPORT 280 -1.637008 0.0298371 0.0262656
GOBP_DEFENSE_RESPONSE_TO_GRAM_NEGATIVE_BACTERIUM 17 -2.120758 0.0302557 0.0266341
GOBP_NEGATIVE_REGULATION_OF_MUSCLE_CELL_DIFFERENTIATION 13 2.052409 0.0302557 0.0266341
GOBP_POSITIVE_REGULATION_OF_PROTEIN_SECRETION 29 2.040795 0.0302557 0.0266341
GOBP_PHOSPHOLIPASE_C_ACTIVATING_G_PROTEIN_COUPLED_RECEPTOR_SIGNALING_PATHWAY 11 2.018056 0.0302557 0.0266341
GOBP_BLOOD_VESSEL_MORPHOGENESIS 110 1.830568 0.0302557 0.0266341
GOBP_VASCULATURE_DEVELOPMENT 131 1.829815 0.0302557 0.0266341
GOBP_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION 122 1.812480 0.0302557 0.0266341
GOBP_RESPONSE_TO_HORMONE 205 1.682103 0.0302557 0.0266341
GOBP_ANIMAL_ORGAN_MORPHOGENESIS 138 1.747786 0.0306542 0.0269849
GOBP_RESPONSE_TO_ORGANIC_CYCLIC_COMPOUND 193 1.733548 0.0306542 0.0269849
GOBP_TISSUE_DEVELOPMENT 348 1.542001 0.0306542 0.0269849
GOBP_CELL_MIGRATION_INVOLVED_IN_SPROUTING_ANGIOGENESIS 10 2.017266 0.0322843 0.0284199
GOBP_ATP_METABOLIC_PROCESS 111 -1.776512 0.0344694 0.0303434
GOBP_CAMERA_TYPE_EYE_DEVELOPMENT 44 1.927631 0.0360847 0.0317653
GOBP_SYNAPSE_ORGANIZATION 71 -1.835258 0.0360847 0.0317653
GOBP_POSITIVE_REGULATION_OF_DEVELOPMENTAL_PROCESS 232 1.623601 0.0372352 0.0327781
GOBP_CYTOKINE_PRODUCTION 147 1.717746 0.0393715 0.0346587
GOBP_CATION_TRANSMEMBRANE_TRANSPORT 155 -1.750186 0.0404780 0.0356328
GOBP_POSITIVE_REGULATION_OF_SIGNALING 341 1.555743 0.0404780 0.0356328
GOBP_RESPONSE_TO_BMP 28 2.066249 0.0415626 0.0365876
GOBP_REGULATION_OF_ENDOTHELIAL_CELL_MIGRATION 28 2.058720 0.0415626 0.0365876
GOBP_REGULATION_OF_MULTICELLULAR_ORGANISMAL_DEVELOPMENT 258 1.581772 0.0415626 0.0365876
GOBP_REGULATION_OF_RESPONSE_TO_STRESS 327 1.568948 0.0415626 0.0365876
GOBP_RESPONSE_TO_OXYGEN_CONTAINING_COMPOUND 336 1.513273 0.0415626 0.0365876
GOBP_POSITIVE_REGULATION_OF_RESPONSE_TO_WOUNDING 12 2.005849 0.0462688 0.0407304
GOBP_ENDOTHELIAL_CELL_APOPTOTIC_PROCESS 13 1.993177 0.0463450 0.0407975
GOBP_TUBE_DEVELOPMENT 199 1.653204 0.0478627 0.0421336
GOBP_ANATOMICAL_STRUCTURE_FORMATION_INVOLVED_IN_MORPHOGENESIS 197 1.641447 0.0478627 0.0421336

ID setSize NES p.adjust qvalue
GOMF_TRANSPORTER_ACTIVITY 260 -2.118267 0.0000211 0.0000194
GOMF_GATED_CHANNEL_ACTIVITY 32 -2.522397 0.0001291 0.0001189
GOMF_PASSIVE_TRANSMEMBRANE_TRANSPORTER_ACTIVITY 61 -2.384464 0.0002468 0.0002274
GOMF_STRUCTURAL_CONSTITUENT_OF_RIBOSOME 99 -2.190401 0.0003165 0.0002916
GOMF_OXIDOREDUCTASE_ACTIVITY_ACTING_ON_NAD_P_H_QUINONE_OR_SIMILAR_COMPOUND_AS_ACCEPTOR 33 -2.404862 0.0004259 0.0003924
GOMF_ION_TRANSMEMBRANE_TRANSPORTER_ACTIVITY 158 -2.018930 0.0007181 0.0006617
GOMF_NADH_DEHYDROGENASE_ACTIVITY 29 -2.385499 0.0009860 0.0009085
GOMF_OXIDOREDUCTION_DRIVEN_ACTIVE_TRANSMEMBRANE_TRANSPORTER_ACTIVITY 45 -2.326842 0.0009860 0.0009085
GOMF_STRUCTURAL_MOLECULE_ACTIVITY 165 -2.025739 0.0009860 0.0009085
GOMF_INORGANIC_MOLECULAR_ENTITY_TRANSMEMBRANE_TRANSPORTER_ACTIVITY 129 -2.079410 0.0013308 0.0012262
GOMF_OXIDOREDUCTASE_ACTIVITY_ACTING_ON_NAD_P_H 35 -2.285747 0.0015349 0.0014142
GOMF_CATION_CHANNEL_ACTIVITY 43 -2.217953 0.0018225 0.0016792
GOMF_VOLTAGE_GATED_CHANNEL_ACTIVITY 18 -2.249661 0.0035844 0.0033026
GOMF_DNA_BINDING_TRANSCRIPTION_ACTIVATOR_ACTIVITY 84 2.024491 0.0035844 0.0033026
GOMF_PRIMARY_ACTIVE_TRANSMEMBRANE_TRANSPORTER_ACTIVITY 65 -2.025923 0.0075539 0.0069600
GOMF_CATION_TRANSMEMBRANE_TRANSPORTER_ACTIVITY 117 -1.899412 0.0147191 0.0135619
GOMF_METAL_ION_TRANSMEMBRANE_TRANSPORTER_ACTIVITY 57 -2.007007 0.0162845 0.0150042
GOMF_ELECTRON_TRANSFER_ACTIVITY 61 -1.882843 0.0224650 0.0206988
GOMF_PROTON_TRANSMEMBRANE_TRANSPORTER_ACTIVITY 45 -2.010496 0.0240866 0.0221929
GOMF_POTASSIUM_ION_TRANSMEMBRANE_TRANSPORTER_ACTIVITY 11 -1.946241 0.0291576 0.0268652
GOMF_PROTON_CHANNEL_ACTIVITY 11 -1.944536 0.0291576 0.0268652
GOMF_CARBOHYDRATE_BINDING 46 -1.987058 0.0292113 0.0269147
GOMF_CALMODULIN_BINDING 31 -1.998581 0.0409216 0.0377044
GOMF_EXTRACELLULAR_MATRIX_STRUCTURAL_CONSTITUENT 15 -1.987028 0.0420049 0.0387025
GOMF_SEQUENCE_SPECIFIC_DNA_BINDING 351 1.483450 0.0420049 0.0387025
GOMF_ACTIVE_TRANSMEMBRANE_TRANSPORTER_ACTIVITY 102 -1.739424 0.0429357 0.0395602

Reactome and Wikipathways

ID setSize NES p.adjust qvalue
REACTOME_RESPIRATORY_ELECTRON_TRANSPORT_ATP_SYNTHESIS_BY_CHEMIOSMOTIC_COUPLING_AND_HEAT_PRODUCTION_BY_UNCOUPLING_PROTEINS 76 -2.288355 0.0046397 0.0045339
REACTOME_CLASS_A_1_RHODOPSIN_LIKE_RECEPTORS 26 2.228044 0.0139838 0.0136648
REACTOME_RESPIRATORY_ELECTRON_TRANSPORT 63 -2.123374 0.0139838 0.0136648
REACTOME_COMPLEX_I_BIOGENESIS 34 -2.239465 0.0186163 0.0181917
REACTOME_EXTRACELLULAR_MATRIX_ORGANIZATION 38 -2.197720 0.0186163 0.0181917
REACTOME_NEURONAL_SYSTEM 60 -2.142954 0.0186163 0.0181917
REACTOME_COLLAGEN_BIOSYNTHESIS_AND_MODIFYING_ENZYMES 10 -2.121133 0.0186163 0.0181917
REACTOME_COLLAGEN_FORMATION 12 -2.099965 0.0482505 0.0471501

ID setSize NES p.adjust qvalue
WP_OXIDATIVE_PHOSPHORYLATION 41 -2.456836 0.0006087 0.0005671
WP_ELECTRON_TRANSPORT_CHAIN_OXPHOS_SYSTEM_IN_MITOCHONDRIA 68 -2.294227 0.0017982 0.0016753
WP_MITOCHONDRIAL_COMPLEX_I_ASSEMBLY_MODEL_OXPHOS_SYSTEM 33 -2.229192 0.0047706 0.0044447
WP_GLUCOCORTICOID_RECEPTOR_PATHWAY 25 2.156775 0.0087083 0.0081134
WP_NUCLEAR_RECEPTORS_METAPATHWAY 78 1.860052 0.0282192 0.0262916
WP_GPCRS_CLASS_A_RHODOPSINLIKE 20 1.999252 0.0377677 0.0351878

Filtering on pval < 0,001

Gene ontology (Biological process and Molecular function)

ID setSize NES p.adjust qvalue
GOBP_POSITIVE_REGULATION_OF_TRANSCRIPTION_BY_RNA_POLYMERASE_II 186 2.520542 0.0000023 0.0000018
GOBP_NEGATIVE_REGULATION_OF_CELL_DIFFERENTIATION 68 2.732333 0.0000192 0.0000149
GOBP_NEGATIVE_REGULATION_OF_DEVELOPMENTAL_PROCESS 98 2.559629 0.0000753 0.0000586
GOBP_NEGATIVE_REGULATION_OF_RESPONSE_TO_STIMULUS 220 2.246038 0.0000837 0.0000652
GOBP_TISSUE_DEVELOPMENT 210 2.240807 0.0000837 0.0000652
GOBP_NEGATIVE_REGULATION_OF_MULTICELLULAR_ORGANISMAL_PROCESS 106 2.493975 0.0001032 0.0000804
GOBP_RESPONSE_TO_ENDOGENOUS_STIMULUS 208 2.242375 0.0001032 0.0000804
GOBP_CELLULAR_RESPONSE_TO_ENDOGENOUS_STIMULUS 179 2.257974 0.0001886 0.0001468
GOBP_MITOCHONDRIAL_RESPIRATORY_CHAIN_COMPLEX_ASSEMBLY 31 -2.902267 0.0002193 0.0001707
GOBP_POSITIVE_REGULATION_OF_RNA_METABOLIC_PROCESS 294 2.060742 0.0002245 0.0001748
GOBP_POSITIVE_REGULATION_OF_NUCLEOBASE_CONTAINING_COMPOUND_METABOLIC_PROCESS 334 2.015989 0.0003228 0.0002513
GOBP_REGULATION_OF_CELLULAR_COMPONENT_MOVEMENT 116 2.314863 0.0003512 0.0002734
GOBP_NADH_DEHYDROGENASE_COMPLEX_ASSEMBLY 20 -2.715416 0.0003646 0.0002838
GOBP_REGULATION_OF_EPITHELIAL_TO_MESENCHYMAL_TRANSITION 12 2.497623 0.0003646 0.0002838
GOBP_CELL_MIGRATION 150 2.206405 0.0003646 0.0002838
GOBP_NEGATIVE_REGULATION_OF_SIGNALING 190 2.145443 0.0003646 0.0002838
GOBP_OXIDATIVE_PHOSPHORYLATION 58 -2.618687 0.0006103 0.0004751
GOBP_REGULATION_OF_ANATOMICAL_STRUCTURE_MORPHOGENESIS 102 2.275272 0.0007678 0.0005978
GOBP_TUBE_DEVELOPMENT 112 2.261188 0.0007678 0.0005978
GOBP_REGULATION_OF_MULTICELLULAR_ORGANISMAL_DEVELOPMENT 150 2.151771 0.0007678 0.0005978
GOBP_LOCOMOTION 187 2.113294 0.0007727 0.0006016
GOBP_RESPONSE_TO_GROWTH_FACTOR 84 2.374888 0.0008212 0.0006393
GOBP_RESPONSE_TO_MECHANICAL_STIMULUS 18 2.483991 0.0009849 0.0007668
GOBP_NEUROGENESIS 177 2.084765 0.0010523 0.0008193
GOBP_CAMERA_TYPE_EYE_DEVELOPMENT 31 2.493461 0.0010657 0.0008297
GOBP_MESENCHYME_DEVELOPMENT 29 2.410737 0.0014483 0.0011276
GOBP_REGULATION_OF_CELL_POPULATION_PROLIFERATION 196 2.048289 0.0014646 0.0011402
GOBP_POSITIVE_REGULATION_OF_CELLULAR_BIOSYNTHETIC_PROCESS 326 1.831229 0.0015698 0.0012222
GOBP_NEURON_DIFFERENTIATION 152 2.093241 0.0019606 0.0015264
GOBP_POSITIVE_REGULATION_OF_DEVELOPMENTAL_PROCESS 147 2.137894 0.0022835 0.0017778
GOBP_REGULATION_OF_CELL_DIFFERENTIATION 173 2.035481 0.0023444 0.0018253
GOBP_MITOCHONDRIAL_ELECTRON_TRANSPORT_NADH_TO_UBIQUINONE 25 -2.578243 0.0023529 0.0018318
GOBP_HOMEOSTATIC_PROCESS 215 1.975803 0.0023529 0.0018318
GOBP_RESPONSE_TO_HORMONE 125 2.092701 0.0032108 0.0024997
GOBP_NEGATIVE_REGULATION_OF_MAP_KINASE_ACTIVITY 16 2.329886 0.0035209 0.0027412
GOBP_ELECTRON_TRANSPORT_CHAIN 49 -2.400410 0.0036033 0.0028054
GOBP_EPITHELIAL_TO_MESENCHYMAL_TRANSITION 22 2.390719 0.0036033 0.0028054
GOBP_MESENCHYMAL_CELL_DIFFERENTIATION 26 2.380425 0.0038034 0.0029611
GOBP_SENSORY_ORGAN_DEVELOPMENT 52 2.271837 0.0038034 0.0029611
GOBP_VASCULATURE_DEVELOPMENT 79 2.148447 0.0050353 0.0039202
GOBP_RESPONSE_TO_OXYGEN_CONTAINING_COMPOUND 208 1.919017 0.0050353 0.0039202
GOBP_ANIMAL_ORGAN_MORPHOGENESIS 78 2.190327 0.0051072 0.0039762
GOBP_MULTICELLULAR_ORGANISM_REPRODUCTION 92 2.132086 0.0051072 0.0039762
GOBP_POSITIVE_REGULATION_OF_MULTICELLULAR_ORGANISMAL_PROCESS 162 2.002985 0.0051072 0.0039762
GOBP_TRANSMEMBRANE_RECEPTOR_PROTEIN_SERINE_THREONINE_KINASE_SIGNALING_PATHWAY 44 2.296290 0.0052264 0.0040690
GOBP_SKELETAL_SYSTEM_DEVELOPMENT 51 2.209678 0.0052264 0.0040690
GOBP_SENSORY_SYSTEM_DEVELOPMENT 38 2.225467 0.0054976 0.0042802
GOBP_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION 75 2.155797 0.0054976 0.0042802
GOBP_RESPIRATORY_ELECTRON_TRANSPORT_CHAIN 43 -2.324364 0.0057177 0.0044515
GOBP_NEGATIVE_REGULATION_OF_LOCOMOTION 43 2.251427 0.0057800 0.0045000
GOBP_MORPHOGENESIS_OF_A_BRANCHING_STRUCTURE 14 2.292658 0.0067662 0.0052678
GOBP_REGULATION_OF_EPITHELIAL_CELL_APOPTOTIC_PROCESS 13 2.267729 0.0067662 0.0052678
GOBP_CELLULAR_RESPONSE_TO_OXYGEN_LEVELS 29 2.221354 0.0067662 0.0052678
GOBP_TUBE_MORPHOGENESIS 87 2.137387 0.0067662 0.0052678
GOBP_ATP_SYNTHESIS_COUPLED_ELECTRON_TRANSPORT 42 -2.285038 0.0071070 0.0055332
GOBP_ADENYLATE_CYCLASE_MODULATING_G_PROTEIN_COUPLED_RECEPTOR_SIGNALING_PATHWAY 12 2.214943 0.0072221 0.0056227
GOBP_ATP_SYNTHESIS_COUPLED_PROTON_TRANSPORT 12 -2.378883 0.0077794 0.0060566
GOBP_EMBRYONIC_MORPHOGENESIS 67 2.108363 0.0077794 0.0060566
GOBP_RESPONSE_TO_PURINE_CONTAINING_COMPOUND 12 2.207272 0.0079176 0.0061642
GOBP_RESPONSE_TO_ORGANIC_CYCLIC_COMPOUND 120 1.995397 0.0086019 0.0066970
GOBP_DEVELOPMENTAL_GROWTH 79 2.047713 0.0111405 0.0086734
GOBP_CIRCULATORY_SYSTEM_DEVELOPMENT 118 2.005901 0.0111405 0.0086734
GOBP_NEGATIVE_REGULATION_OF_MAPK_CASCADE 34 2.218943 0.0112981 0.0087961
GOBP_REGULATION_OF_CELL_DEATH 237 1.814680 0.0122565 0.0095423
GOBP_ANATOMICAL_STRUCTURE_FORMATION_INVOLVED_IN_MORPHOGENESIS 106 1.967618 0.0128013 0.0099664
GOBP_EPITHELIAL_CELL_APOPTOTIC_PROCESS 19 2.184513 0.0135031 0.0105128
GOBP_STRIATED_MUSCLE_CELL_PROLIFERATION 10 2.175729 0.0139482 0.0108593
GOBP_RESPONSE_TO_FIBROBLAST_GROWTH_FACTOR 13 2.173198 0.0150453 0.0117135
GOBP_EPIDERMAL_CELL_DIFFERENTIATION 23 2.203935 0.0166580 0.0129691
GOBP_REGULATION_OF_IMMUNE_SYSTEM_PROCESS 159 1.862746 0.0169462 0.0131934
GOBP_SENSORY_ORGAN_MORPHOGENESIS 22 2.181919 0.0171615 0.0133610
GOBP_REGULATION_OF_CELLULAR_RESPONSE_TO_GROWTH_FACTOR_STIMULUS 35 2.130150 0.0171615 0.0133610
GOBP_TRANSFORMING_GROWTH_FACTOR_BETA_RECEPTOR_SIGNALING_PATHWAY 29 2.101218 0.0171615 0.0133610
GOBP_REPRODUCTIVE_SYSTEM_DEVELOPMENT 64 2.057835 0.0171615 0.0133610
GOBP_IMMUNE_SYSTEM_DEVELOPMENT 127 1.940871 0.0171615 0.0133610
GOBP_RESPONSE_TO_ABIOTIC_STIMULUS 152 1.875930 0.0171615 0.0133610
GOBP_ATP_BIOSYNTHETIC_PROCESS 18 -2.310544 0.0172041 0.0133942
GOBP_BLOOD_VESSEL_MORPHOGENESIS 67 2.008110 0.0172041 0.0133942
GOBP_DEVELOPMENTAL_PROCESS_INVOLVED_IN_REPRODUCTION 109 1.959445 0.0172041 0.0133942
GOBP_RESPONSE_TO_OXYGEN_LEVELS 43 2.074108 0.0183047 0.0142511
GOBP_CELLULAR_RESPONSE_TO_CHEMICAL_STRESS 58 2.020766 0.0183047 0.0142511
GOBP_RESPONSE_TO_LIPID 104 1.915768 0.0183047 0.0142511
GOBP_HOMEOSTASIS_OF_NUMBER_OF_CELLS 46 2.110086 0.0187368 0.0145875
GOBP_NEGATIVE_REGULATION_OF_CELL_POPULATION_PROLIFERATION 83 2.005431 0.0192951 0.0150222
GOBP_RETINA_DEVELOPMENT_IN_CAMERA_TYPE_EYE 14 2.148009 0.0201646 0.0156991
GOBP_CELLULAR_RESPIRATION 70 -2.101503 0.0210723 0.0164058
GOBP_CONNECTIVE_TISSUE_DEVELOPMENT 29 2.049929 0.0221556 0.0172492
GOBP_PATTERN_RECOGNITION_RECEPTOR_SIGNALING_PATHWAY 24 2.143411 0.0231697 0.0180387
GOBP_REGULATION_OF_VASCULATURE_DEVELOPMENT 34 2.082821 0.0231697 0.0180387
GOBP_GAMETE_GENERATION 75 1.962863 0.0238059 0.0185340
GOBP_RAS_PROTEIN_SIGNAL_TRANSDUCTION 57 1.975841 0.0244657 0.0190477
GOBP_MULTI_ORGANISM_REPRODUCTIVE_PROCESS 108 1.915803 0.0246667 0.0192042
GOBP_REGULATION_OF_RESPONSE_TO_STRESS 213 1.741558 0.0246667 0.0192042
GOBP_PROTON_TRANSMEMBRANE_TRANSPORT 37 -2.194737 0.0247802 0.0192925
GOBP_EXPORT_FROM_CELL 100 1.902364 0.0247802 0.0192925
GOBP_POSITIVE_REGULATION_OF_CELL_DEATH 83 1.958853 0.0251349 0.0195687
GOBP_INFLAMMATORY_RESPONSE 79 1.937189 0.0251349 0.0195687
GOBP_CELLULAR_RESPONSE_TO_HORMONE_STIMULUS 94 1.912203 0.0281838 0.0219424
GOBP_AEROBIC_RESPIRATION 68 -2.065190 0.0283058 0.0220374
GOBP_NEGATIVE_REGULATION_OF_INTRACELLULAR_SIGNAL_TRANSDUCTION 93 1.909516 0.0305657 0.0237968
GOBP_IMMUNE_RESPONSE_REGULATING_SIGNALING_PATHWAY 46 2.038982 0.0309432 0.0240908
GOBP_ATP_METABOLIC_PROCESS 80 -1.986259 0.0309432 0.0240908
GOBP_DEFENSE_RESPONSE_TO_GRAM_NEGATIVE_BACTERIUM 11 -2.170584 0.0328693 0.0255903
GOBP_NEGATIVE_REGULATION_OF_NEURON_DIFFERENTIATION 10 2.073273 0.0328693 0.0255903
GOBP_CENTRAL_NERVOUS_SYSTEM_NEURON_DIFFERENTIATION 18 2.065049 0.0336125 0.0261689
GOBP_EMBRYONIC_ORGAN_DEVELOPMENT 44 2.052500 0.0336125 0.0261689
GOBP_DIGESTIVE_SYSTEM_DEVELOPMENT 12 2.008951 0.0336125 0.0261689
GOBP_REGULATION_OF_TRANSMEMBRANE_RECEPTOR_PROTEIN_SERINE_THREONINE_KINASE_SIGNALING_PATHWAY 31 2.047995 0.0339652 0.0264435
GOBP_POSITIVE_REGULATION_OF_LOCOMOTION 62 1.987559 0.0340929 0.0265429
GOBP_EPITHELIAL_CELL_DIFFERENTIATION 79 1.877152 0.0347002 0.0270157
GOBP_REGIONALIZATION 27 2.077870 0.0347593 0.0270618
GOBP_MITOCHONDRIAL_TRANSLATION 27 -2.135346 0.0347906 0.0270861
GOBP_FORMATION_OF_PRIMARY_GERM_LAYER 10 2.061688 0.0347906 0.0270861
GOBP_INTRACELLULAR_RECEPTOR_SIGNALING_PATHWAY 37 2.041454 0.0351024 0.0273289
GOBP_NEGATIVE_REGULATION_OF_CELLULAR_RESPONSE_TO_GROWTH_FACTOR_STIMULUS 14 2.062521 0.0354129 0.0275706
GOBP_RESPONSE_TO_TRANSFORMING_GROWTH_FACTOR_BETA 37 2.030162 0.0354129 0.0275706
GOBP_PATTERN_SPECIFICATION_PROCESS 37 2.009629 0.0354129 0.0275706
GOBP_NEURON_DEVELOPMENT 119 1.823696 0.0354129 0.0275706
GOBP_CHEMICAL_HOMEOSTASIS 125 1.801176 0.0354129 0.0275706
GOBP_CELL_PROJECTION_ORGANIZATION 187 1.724185 0.0354129 0.0275706
GOBP_CENTRAL_NERVOUS_SYSTEM_DEVELOPMENT 120 1.802491 0.0367372 0.0286016
GOBP_REGULATION_OF_RECEPTOR_MEDIATED_ENDOCYTOSIS 16 1.970186 0.0369300 0.0287518
GOBP_MUSCLE_TISSUE_DEVELOPMENT 47 1.947823 0.0369300 0.0287518
GOBP_NEGATIVE_REGULATION_OF_GENE_EXPRESSION 176 1.733051 0.0369300 0.0287518
GOBP_REGULATION_OF_PATTERN_RECOGNITION_RECEPTOR_SIGNALING_PATHWAY 19 2.011395 0.0376068 0.0292787
GOBP_VESICLE_BUDDING_FROM_MEMBRANE 17 1.982380 0.0376068 0.0292787
GOBP_PLACENTA_DEVELOPMENT 22 1.973725 0.0376068 0.0292787
GOBP_REGULATION_OF_HEMOPOIESIS 49 1.940625 0.0376068 0.0292787
GOBP_REGULATION_OF_VESICLE_MEDIATED_TRANSPORT 61 1.931273 0.0376068 0.0292787
GOBP_CYTOKINE_PRODUCTION 85 1.831798 0.0376068 0.0292787
GOBP_GASTRULATION 22 2.033972 0.0379759 0.0295660
GOBP_MUSCLE_CELL_PROLIFERATION 24 2.031813 0.0379759 0.0295660
GOBP_GLIAL_CELL_DIFFERENTIATION 17 2.010595 0.0379759 0.0295660
GOBP_CELLULAR_RESPONSE_TO_KETONE 17 2.009885 0.0379759 0.0295660
GOBP_CARDIOCYTE_DIFFERENTIATION 22 1.967948 0.0379759 0.0295660
GOBP_NUCLEOSIDE_BISPHOSPHATE_METABOLIC_PROCESS 17 1.967332 0.0379759 0.0295660
GOBP_CELL_FATE_COMMITMENT 21 1.960722 0.0379759 0.0295660
GOBP_MATERNAL_PROCESS_INVOLVED_IN_FEMALE_PREGNANCY 11 1.959295 0.0379759 0.0295660
GOBP_RESPONSE_TO_NITROGEN_COMPOUND 162 1.706538 0.0379759 0.0295660
GOBP_P38MAPK_CASCADE 10 1.943107 0.0383725 0.0298748
GOBP_GROWTH 131 1.783223 0.0383725 0.0298748
GOBP_EYE_MORPHOGENESIS 14 1.945231 0.0384745 0.0299543
GOBP_NEGATIVE_REGULATION_OF_PROTEIN_SERINE_THREONINE_KINASE_ACTIVITY 27 1.957757 0.0390816 0.0304269
GOBP_EMBRYONIC_ORGAN_MORPHOGENESIS 27 2.037600 0.0392192 0.0305340
GOBP_RESPONSE_TO_STEROID_HORMONE 52 1.933761 0.0392192 0.0305340
GOBP_REGENERATION 23 2.038253 0.0393878 0.0306653
GOBP_RHYTHMIC_PROCESS 42 1.912733 0.0393878 0.0306653
GOBP_MITOCHONDRION_ORGANIZATION 115 -1.826157 0.0393878 0.0306653
GOBP_REGULATION_OF_CELL_ADHESION 79 1.817432 0.0393878 0.0306653
GOBP_TOLL_LIKE_RECEPTOR_SIGNALING_PATHWAY 17 1.994817 0.0395308 0.0307766
GOBP_MAPK_CASCADE 103 1.806639 0.0404445 0.0314880
GOBP_CELL_SURFACE_RECEPTOR_SIGNALING_PATHWAY_INVOLVED_IN_CELL_CELL_SIGNALING 65 1.866532 0.0411553 0.0320413
GOBP_REGULATION_OF_WNT_SIGNALING_PATHWAY 41 1.916576 0.0415834 0.0323747
GOBP_RESPONSE_TO_BMP 18 1.998648 0.0417595 0.0325118
GOBP_MYELOID_CELL_HOMEOSTASIS 34 1.939586 0.0419168 0.0326343
GOBP_NUCLEOSIDE_TRIPHOSPHATE_BIOSYNTHETIC_PROCESS 26 -2.067213 0.0421505 0.0328162
GOBP_CARDIAC_VENTRICLE_DEVELOPMENT 13 1.953341 0.0421505 0.0328162
GOBP_CELL_MORPHOGENESIS 110 1.782037 0.0421505 0.0328162
GOBP_CYTOCHROME_COMPLEX_ASSEMBLY 11 -2.097267 0.0423384 0.0329625
GOBP_LEUKOCYTE_HOMEOSTASIS 11 2.022166 0.0423384 0.0329625
GOBP_REGULATION_OF_EPITHELIAL_CELL_MIGRATION 22 1.931923 0.0423384 0.0329625
GOBP_SULFUR_COMPOUND_BIOSYNTHETIC_PROCESS 27 1.929549 0.0423384 0.0329625
GOBP_RIBONUCLEOSIDE_TRIPHOSPHATE_BIOSYNTHETIC_PROCESS 25 -2.106270 0.0424666 0.0330623
GOBP_CELLULAR_RESPONSE_TO_STEROID_HORMONE_STIMULUS 36 1.925162 0.0424666 0.0330623
GOBP_CARDIAC_SEPTUM_DEVELOPMENT 10 1.912676 0.0454562 0.0353898
GOBP_REGULATION_OF_SECRETION 66 1.832455 0.0454562 0.0353898
GOBP_EPITHELIUM_DEVELOPMENT 123 1.745447 0.0454562 0.0353898
GOBP_REPRODUCTION 171 1.655858 0.0454562 0.0353898
GOBP_HEART_GROWTH 12 1.941074 0.0458155 0.0356696
GOBP_CAMERA_TYPE_EYE_MORPHOGENESIS 11 1.912970 0.0459074 0.0357411
GOBP_REGULATION_OF_TOLL_LIKE_RECEPTOR_SIGNALING_PATHWAY 15 1.926190 0.0459104 0.0357434
GOBP_CELLULAR_RESPONSE_TO_MECHANICAL_STIMULUS 10 1.909144 0.0459918 0.0358068
GOBP_POSITIVE_REGULATION_OF_MYELOID_CELL_DIFFERENTIATION 20 1.895228 0.0459918 0.0358068
GOBP_CARDIAC_CHAMBER_MORPHOGENESIS 10 1.976894 0.0466138 0.0362911
GOBP_POSITIVE_REGULATION_OF_VASCULATURE_DEVELOPMENT 19 1.909194 0.0468622 0.0364845
GOBP_SYNAPTIC_SIGNALING 64 -1.905223 0.0468622 0.0364845
GOBP_NEGATIVE_REGULATION_OF_RESPONSE_TO_EXTERNAL_STIMULUS 41 1.879225 0.0470050 0.0365956
GOBP_RESPONSE_TO_MOLECULE_OF_BACTERIAL_ORIGIN 27 1.905341 0.0470955 0.0366661
GOBP_ENDOTHELIAL_CELL_DEVELOPMENT 15 -2.025903 0.0471560 0.0367132
GOBP_BRANCHING_MORPHOGENESIS_OF_AN_EPITHELIAL_TUBE 10 1.898611 0.0471560 0.0367132
GOBP_CELLULAR_RESPONSE_TO_OXYGEN_CONTAINING_COMPOUND 148 1.696419 0.0476757 0.0371178
GOBP_REGULATION_OF_MITOCHONDRIAL_GENE_EXPRESSION 10 -2.039005 0.0478544 0.0372570
GOBP_NEGATIVE_REGULATION_OF_INFLAMMATORY_RESPONSE 20 1.887775 0.0478544 0.0372570
GOBP_REGULATION_OF_SMALL_GTPASE_MEDIATED_SIGNAL_TRANSDUCTION 37 1.889081 0.0486031 0.0378399
GOBP_RECEPTOR_MEDIATED_ENDOCYTOSIS 35 1.897636 0.0492094 0.0383119
GOBP_ERK1_AND_ERK2_CASCADE 33 1.892530 0.0492094 0.0383119
GOBP_NEGATIVE_REGULATION_OF_CYTOKINE_PRODUCTION 33 1.891862 0.0492094 0.0383119
GOBP_GENE_SILENCING_BY_RNA 27 1.886893 0.0492094 0.0383119
GOBP_RESPONSE_TO_PEPTIDE 74 1.784201 0.0492919 0.0383761

ID setSize NES p.adjust qvalue
GOMF_STRUCTURAL_CONSTITUENT_OF_RIBOSOME 79 -3.188977 0.0000001 0.0000001
GOMF_OXIDOREDUCTASE_ACTIVITY_ACTING_ON_NAD_P_H_QUINONE_OR_SIMILAR_COMPOUND_AS_ACCEPTOR 25 -2.913449 0.0000317 0.0000277
GOMF_OXIDOREDUCTION_DRIVEN_ACTIVE_TRANSMEMBRANE_TRANSPORTER_ACTIVITY 34 -2.872495 0.0000317 0.0000277
GOMF_NADH_DEHYDROGENASE_ACTIVITY 22 -2.804994 0.0001147 0.0001004
GOMF_OXIDOREDUCTASE_ACTIVITY_ACTING_ON_NAD_P_H 27 -2.757845 0.0001527 0.0001336
GOMF_SEQUENCE_SPECIFIC_DNA_BINDING 204 2.161929 0.0001527 0.0001336
GOMF_DNA_BINDING_TRANSCRIPTION_FACTOR_ACTIVITY 132 2.239072 0.0002665 0.0002331
GOMF_CIS_REGULATORY_REGION_SEQUENCE_SPECIFIC_DNA_BINDING 120 2.263349 0.0002898 0.0002535
GOMF_ELECTRON_TRANSFER_ACTIVITY 44 -2.635098 0.0003119 0.0002728
GOMF_STRUCTURAL_MOLECULE_ACTIVITY 117 -2.279298 0.0003119 0.0002728
GOMF_TRANSCRIPTION_REGULATOR_ACTIVITY 228 1.997992 0.0005922 0.0005180
GOMF_TRANSPORTER_ACTIVITY 141 -2.159188 0.0008350 0.0007303
GOMF_DNA_BINDING_TRANSCRIPTION_ACTIVATOR_ACTIVITY 50 2.301884 0.0011857 0.0010371
GOMF_PRIMARY_ACTIVE_TRANSMEMBRANE_TRANSPORTER_ACTIVITY 43 -2.420557 0.0016916 0.0014796
GOMF_RRNA_BINDING 22 -2.125691 0.0439659 0.0384556

Reactome and Wikipathways

ID setSize NES p.adjust qvalue
REACTOME_RESPIRATORY_ELECTRON_TRANSPORT_ATP_SYNTHESIS_BY_CHEMIOSMOTIC_COUPLING_AND_HEAT_PRODUCTION_BY_UNCOUPLING_PROTEINS 57 -2.914298 0.0000390 0.0000371
REACTOME_COMPLEX_I_BIOGENESIS 24 -2.745282 0.0003135 0.0002980
REACTOME_EUKARYOTIC_TRANSLATION_ELONGATION 50 -2.683024 0.0003135 0.0002980
REACTOME_INFLUENZA_INFECTION 61 -2.627043 0.0003135 0.0002980
REACTOME_TRANSLATION 122 -2.405331 0.0003135 0.0002980
REACTOME_RESPIRATORY_ELECTRON_TRANSPORT 46 -2.633468 0.0003681 0.0003500
REACTOME_THE_CITRIC_ACID_TCA_CYCLE_AND_RESPIRATORY_ELECTRON_TRANSPORT 67 -2.430707 0.0012242 0.0011638
REACTOME_SRP_DEPENDENT_COTRANSLATIONAL_PROTEIN_TARGETING_TO_MEMBRANE 58 -2.441586 0.0012949 0.0012311
REACTOME_MITOCHONDRIAL_TRANSLATION 36 -2.599831 0.0014253 0.0013550
REACTOME_RESPONSE_OF_EIF2AK4_GCN2_TO_AMINO_ACID_DEFICIENCY 52 -2.387285 0.0019799 0.0018823
REACTOME_REGULATION_OF_EXPRESSION_OF_SLITS_AND_ROBOS 76 -2.276734 0.0030012 0.0028532
REACTOME_CELLULAR_RESPONSE_TO_STARVATION 65 -2.255515 0.0032817 0.0031199
REACTOME_RRNA_PROCESSING 90 -2.178627 0.0032817 0.0031199
REACTOME_SELENOAMINO_ACID_METABOLISM 53 -2.222195 0.0060371 0.0057393
REACTOME_SIGNALING_BY_ROBO_RECEPTORS 80 -2.085943 0.0086215 0.0081963
REACTOME_TOLL_LIKE_RECEPTOR_CASCADES 23 2.145401 0.0160538 0.0152621
REACTOME_NEURONAL_SYSTEM 32 -2.181792 0.0258105 0.0245375
REACTOME_NONSENSE_MEDIATED_DECAY_NMD 59 -2.121582 0.0258105 0.0245375
REACTOME_REGULATION_OF_CHOLESTEROL_BIOSYNTHESIS_BY_SREBP_SREBF 16 2.046887 0.0258105 0.0245375
REACTOME_EUKARYOTIC_TRANSLATION_INITIATION 59 -2.061974 0.0307471 0.0292307

ID setSize NES p.adjust qvalue
WP_OXIDATIVE_PHOSPHORYLATION 33 -3.016538 0.0000067 0.0000057
WP_ELECTRON_TRANSPORT_CHAIN_OXPHOS_SYSTEM_IN_MITOCHONDRIA 54 -2.851399 0.0000090 0.0000075
WP_MITOCHONDRIAL_COMPLEX_I_ASSEMBLY_MODEL_OXPHOS_SYSTEM 23 -2.739863 0.0004285 0.0003602
WP_CYTOPLASMIC_RIBOSOMAL_PROTEINS 49 -2.524652 0.0008650 0.0007271
WP_GLUCOCORTICOID_RECEPTOR_PATHWAY 17 2.154503 0.0126969 0.0106722
WP_FRAGILE_X_SYNDROME 18 -2.073289 0.0400842 0.0336921
WP_STEROL_REGULATORY_ELEMENTBINDING_PROTEINS_SREBP_SIGNALING 20 2.066070 0.0400842 0.0336921
WP_NONALCOHOLIC_FATTY_LIVER_DISEASE 46 -1.978519 0.0400842 0.0336921
WP_NUCLEAR_RECEPTORS_METAPATHWAY 52 1.964658 0.0400842 0.0336921
WP_SUDDEN_INFANT_DEATH_SYNDROME_SIDS_SUSCEPTIBILITY_PATHWAYS 17 2.030388 0.0444559 0.0373667
WP_ARYL_HYDROCARBON_RECEPTOR_PATHWAY_WP2586 13 1.986317 0.0444559 0.0373667
WP_CIRCADIAN_RHYTHM_GENES 34 1.940488 0.0444559 0.0373667

Test specific targets

Load the GO annotations for the antigen presenting pathway (GO:0019882)

Highlight on the volcano plot of the genes found to be implicated in the antigen presenting pathway + table

gene log2FoldChange padj description
RAB8B 1.3082949 0.0000000 RAB8B, member RAS oncogene family [Source:HGNC Symbol;Acc:HGNC:30273]
RAB35 0.9675892 0.0000000 RAB35, member RAS oncogene family [Source:HGNC Symbol;Acc:HGNC:9774]
LNPEP 1.1727759 0.0000000 leucyl and cystinyl aminopeptidase [Source:HGNC Symbol;Acc:HGNC:6656]
ARL8B 0.7914131 0.0000000 ADP ribosylation factor like GTPase 8B [Source:HGNC Symbol;Acc:HGNC:25564]
PIKFYVE 0.8594568 0.0000001 phosphoinositide kinase, FYVE-type zinc finger containing [Source:HGNC Symbol;Acc:HGNC:23785]
CTSD -0.6241187 0.0000027 cathepsin D [Source:HGNC Symbol;Acc:HGNC:2529]
ERAP2 -0.8017025 0.0000048 endoplasmic reticulum aminopeptidase 2 [Source:HGNC Symbol;Acc:HGNC:29499]
RAB33A 1.3929028 0.0000133 RAB33A, member RAS oncogene family [Source:HGNC Symbol;Acc:HGNC:9773]
RAB6A 0.5461231 0.0000417 RAB6A, member RAS oncogene family [Source:HGNC Symbol;Acc:HGNC:9786]
MICA -0.6871788 0.0000464 MHC class I polypeptide-related sequence A [Source:HGNC Symbol;Acc:HGNC:7090]
FCGR1A -1.0134651 0.0001062 Fc gamma receptor Ia [Source:HGNC Symbol;Acc:HGNC:3613]
ERAP1 0.5559485 0.0005007 endoplasmic reticulum aminopeptidase 1 [Source:HGNC Symbol;Acc:HGNC:18173]

Crossing with immunopeptidomic data

Table of the genes that could be found as proteins in the significantly enriched peptides in the immunopeptidomic data.

## [1] 36 11
gene log2FoldChange padj description
KRTCAP2 -1.5021573 0.0000000 keratinocyte associated protein 2 [Source:HGNC Symbol;Acc:HGNC:28942]
PRTN3 -1.2107807 0.0000000 proteinase 3 [Source:HGNC Symbol;Acc:HGNC:9495]
METAP2 1.1040167 0.0000000 methionyl aminopeptidase 2 [Source:HGNC Symbol;Acc:HGNC:16672]
RPL35 -1.1732016 0.0000000 ribosomal protein L35 [Source:HGNC Symbol;Acc:HGNC:10344]
ELANE -1.2322149 0.0000000 elastase, neutrophil expressed [Source:HGNC Symbol;Acc:HGNC:3309]
PXK 1.1528337 0.0000000 PX domain containing serine/threonine kinase like [Source:HGNC Symbol;Acc:HGNC:23326]
RBMX 0.9197177 0.0000000 RNA binding motif protein X-linked [Source:HGNC Symbol;Acc:HGNC:9910]
PPP1R27 -1.4553395 0.0000000 protein phosphatase 1 regulatory subunit 27 [Source:HGNC Symbol;Acc:HGNC:16813]
PMF1 -0.8998079 0.0000000 polyamine modulated factor 1 [Source:HGNC Symbol;Acc:HGNC:9112]
ATP5PF -0.9758286 0.0000000 ATP synthase peripheral stalk subunit F6 [Source:HGNC Symbol;Acc:HGNC:847]
TSTD2 2.0711363 0.0000000 thiosulfate sulfurtransferase like domain containing 2 [Source:HGNC Symbol;Acc:HGNC:30087]
TGS1 1.1872364 0.0000000 trimethylguanosine synthase 1 [Source:HGNC Symbol;Acc:HGNC:17843]
PRPF31 -0.9557415 0.0000000 pre-mRNA processing factor 31 [Source:HGNC Symbol;Acc:HGNC:15446]
TXNIP 1.2337513 0.0000000 thioredoxin interacting protein [Source:HGNC Symbol;Acc:HGNC:16952]
DNAJA2 1.0801674 0.0000000 DnaJ heat shock protein family (Hsp40) member A2 [Source:HGNC Symbol;Acc:HGNC:14884]
BCLAF1 0.6766773 0.0000000 BCL2 associated transcription factor 1 [Source:HGNC Symbol;Acc:HGNC:16863]
RPS17 -0.7267731 0.0000000 ribosomal protein S17 [Source:HGNC Symbol;Acc:HGNC:10397]
TRIM13 -0.7992741 0.0000000 tripartite motif containing 13 [Source:HGNC Symbol;Acc:HGNC:9976]
LNPEP 1.1727759 0.0000000 leucyl and cystinyl aminopeptidase [Source:HGNC Symbol;Acc:HGNC:6656]
MTA2 -0.7637732 0.0000000 metastasis associated 1 family member 2 [Source:HGNC Symbol;Acc:HGNC:7411]
NA 3.2170778 0.0000000 novel transcript
RPL34 -0.7593908 0.0000000 ribosomal protein L34 [Source:HGNC Symbol;Acc:HGNC:10340]
NA 4.5353284 0.0000003 novel transcript, antisense to RPTOR
PPT1 1.1207877 0.0000003 palmitoyl-protein thioesterase 1 [Source:HGNC Symbol;Acc:HGNC:9325]
ATP5F1B 0.8913198 0.0000003 ATP synthase F1 subunit beta [Source:HGNC Symbol;Acc:HGNC:830]
TUBB4B -0.8346326 0.0000007 tubulin beta 4B class IVb [Source:HGNC Symbol;Acc:HGNC:20771]
ABHD17B 0.8712265 0.0000041 abhydrolase domain containing 17B, depalmitoylase [Source:HGNC Symbol;Acc:HGNC:24278]
METAP1 0.5845978 0.0000131 methionyl aminopeptidase 1 [Source:HGNC Symbol;Acc:HGNC:15789]
GFPT1 0.7942751 0.0000173 glutamine–fructose-6-phosphate transaminase 1 [Source:HGNC Symbol;Acc:HGNC:4241]
CIRBP -0.4092358 0.0002673 cold inducible RNA binding protein [Source:HGNC Symbol;Acc:HGNC:1982]
COPZ1 -0.4227278 0.0003366 COPI coat complex subunit zeta 1 [Source:HGNC Symbol;Acc:HGNC:2243]
CAD -0.5876069 0.0003795 carbamoyl-phosphate synthetase 2, aspartate transcarbamylase, and dihydroorotase [Source:HGNC Symbol;Acc:HGNC:1424]
CDK17 0.6835569 0.0005126 cyclin dependent kinase 17 [Source:HGNC Symbol;Acc:HGNC:8750]
FASN 0.4674484 0.0007743 fatty acid synthase [Source:HGNC Symbol;Acc:HGNC:3594]
PSMD7 0.5346745 0.0008086 proteasome 26S subunit, non-ATPase 7 [Source:HGNC Symbol;Acc:HGNC:9565]
HNRNPDL 0.3766856 0.0009490 heterogeneous nuclear ribonucleoprotein D like [Source:HGNC Symbol;Acc:HGNC:5037]

Crossing with the proteomics data

## [1] 19 11
gene log2FoldChange padj description
CD63 -1.0314250 0.0000000 CD63 molecule [Source:HGNC Symbol;Acc:HGNC:1692]
LMAN1 1.1586409 0.0000000 lectin, mannose binding 1 [Source:HGNC Symbol;Acc:HGNC:6631]
SRGN 1.0732210 0.0000000 serglycin [Source:HGNC Symbol;Acc:HGNC:9361]
ERP29 -0.7739467 0.0000000 endoplasmic reticulum protein 29 [Source:HGNC Symbol;Acc:HGNC:13799]
FDFT1 0.8132262 0.0000000 farnesyl-diphosphate farnesyltransferase 1 [Source:HGNC Symbol;Acc:HGNC:3629]
SEPTIN6 0.8225595 0.0000000 septin 6 [Source:HGNC Symbol;Acc:HGNC:15848]
CRELD2 -0.7833789 0.0000000 cysteine rich with EGF like domains 2 [Source:HGNC Symbol;Acc:HGNC:28150]
TMED2 0.8504556 0.0000000 transmembrane p24 trafficking protein 2 [Source:HGNC Symbol;Acc:HGNC:16996]
NA 3.2170778 0.0000000 novel transcript
SSR1 0.6722112 0.0000002 signal sequence receptor subunit 1 [Source:HGNC Symbol;Acc:HGNC:11323]
NA 4.5353284 0.0000003 novel transcript, antisense to RPTOR
CTDSPL2 0.8425381 0.0000021 CTD small phosphatase like 2 [Source:HGNC Symbol;Acc:HGNC:26936]
LIPA 1.1072755 0.0000054 lipase A, lysosomal acid type [Source:HGNC Symbol;Acc:HGNC:6617]
NOMO3 1.7667326 0.0000194 NODAL modulator 3 [Source:HGNC Symbol;Acc:HGNC:25242]
DHX34 -0.6251980 0.0000320 DExH-box helicase 34 [Source:HGNC Symbol;Acc:HGNC:16719]
RPL26 -0.5912310 0.0000644 ribosomal protein L26 [Source:HGNC Symbol;Acc:HGNC:10327]
ALDH1L2 0.7364999 0.0001866 aldehyde dehydrogenase 1 family member L2 [Source:HGNC Symbol;Acc:HGNC:26777]
BCAP31 -0.4427626 0.0002662 B cell receptor associated protein 31 [Source:HGNC Symbol;Acc:HGNC:16695]
GNS 0.6935357 0.0004480 glucosamine (N-acetyl)-6-sulfatase [Source:HGNC Symbol;Acc:HGNC:4422]

Save the data and the environment

Session info

sessionInfo()
## R version 4.2.1 (2022-06-23)
## Platform: x86_64-apple-darwin17.0 (64-bit)
## Running under: macOS Catalina 10.15.7
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.2/Resources/lib/libRlapack.dylib
## 
## locale:
## [1] fr_BE.UTF-8/fr_BE.UTF-8/fr_BE.UTF-8/C/fr_BE.UTF-8/fr_BE.UTF-8
## 
## attached base packages:
## [1] stats     graphics  grDevices utils     datasets  methods   base     
## 
## other attached packages:
##  [1] readxl_1.4.1          msigdbr_7.5.1         clusterProfiler_4.4.4
##  [4] ggrepel_0.9.1         forcats_0.5.2         stringr_1.4.1        
##  [7] dplyr_1.0.10          purrr_0.3.4           readr_2.1.2          
## [10] tidyr_1.2.1           tibble_3.1.8          ggplot2_3.3.6        
## [13] tidyverse_1.3.2      
## 
## loaded via a namespace (and not attached):
##   [1] shadowtext_0.1.2       backports_1.4.1        fastmatch_1.1-3       
##   [4] plyr_1.8.7             igraph_1.3.4           lazyeval_0.2.2        
##   [7] splines_4.2.1          BiocParallel_1.30.3    GenomeInfoDb_1.32.4   
##  [10] digest_0.6.29          yulab.utils_0.0.5      htmltools_0.5.3       
##  [13] GOSemSim_2.22.0        viridis_0.6.2          GO.db_3.15.0          
##  [16] fansi_1.0.3            magrittr_2.0.3         memoise_2.0.1         
##  [19] googlesheets4_1.0.1    tzdb_0.3.0             Biostrings_2.64.1     
##  [22] graphlayouts_0.8.1     modelr_0.1.9           vroom_1.5.7           
##  [25] enrichplot_1.16.2      colorspace_2.0-3       blob_1.2.3            
##  [28] rvest_1.0.3            haven_2.5.1            xfun_0.32             
##  [31] crayon_1.5.1           RCurl_1.98-1.8         jsonlite_1.8.0        
##  [34] scatterpie_0.1.8       ape_5.6-2              glue_1.6.2            
##  [37] polyclip_1.10-0        gtable_0.3.1           gargle_1.2.1          
##  [40] zlibbioc_1.42.0        XVector_0.36.0         BiocGenerics_0.42.0   
##  [43] scales_1.2.1           DOSE_3.22.1            DBI_1.1.3             
##  [46] Rcpp_1.0.9             viridisLite_0.4.1      gridGraphics_0.5-1    
##  [49] tidytree_0.4.0         bit_4.0.4              stats4_4.2.1          
##  [52] httr_1.4.4             fgsea_1.22.0           RColorBrewer_1.1-3    
##  [55] ellipsis_0.3.2         pkgconfig_2.0.3        farver_2.1.1          
##  [58] sass_0.4.2             dbplyr_2.2.1           utf8_1.2.2            
##  [61] ggplotify_0.1.0        tidyselect_1.1.2       labeling_0.4.2        
##  [64] rlang_1.0.5            reshape2_1.4.4         AnnotationDbi_1.58.0  
##  [67] munsell_0.5.0          cellranger_1.1.0       tools_4.2.1           
##  [70] cachem_1.0.6           downloader_0.4         cli_3.4.0             
##  [73] generics_0.1.3         RSQLite_2.2.16         broom_1.0.1           
##  [76] evaluate_0.16          fastmap_1.1.0          yaml_2.3.5            
##  [79] ggtree_3.4.2           babelgene_22.9         knitr_1.40            
##  [82] bit64_4.0.5            fs_1.5.2               tidygraph_1.2.2       
##  [85] KEGGREST_1.36.3        ggraph_2.0.6           nlme_3.1-157          
##  [88] aplot_0.1.7            DO.db_2.9              xml2_1.3.3            
##  [91] compiler_4.2.1         rstudioapi_0.14        png_0.1-7             
##  [94] reprex_2.0.2           treeio_1.20.2          tweenr_2.0.2          
##  [97] bslib_0.4.0            stringi_1.7.8          highr_0.9             
## [100] lattice_0.20-45        Matrix_1.5-1           vctrs_0.4.1           
## [103] pillar_1.8.1           lifecycle_1.0.2        jquerylib_0.1.4       
## [106] data.table_1.14.2      bitops_1.0-7           patchwork_1.1.2       
## [109] qvalue_2.28.0          R6_2.5.1               gridExtra_2.3         
## [112] IRanges_2.30.1         codetools_0.2-18       MASS_7.3-57           
## [115] assertthat_0.2.1       withr_2.5.0            S4Vectors_0.34.0      
## [118] GenomeInfoDbData_1.2.8 parallel_4.2.1         hms_1.1.2             
## [121] grid_4.2.1             ggfun_0.0.7            rmarkdown_2.16        
## [124] googledrive_2.0.0      ggforce_0.3.4          Biobase_2.56.0        
## [127] lubridate_1.8.0